Time Lord Trilogy I Part 1 Version 2
by ClaraSouffleOswald
Summary: This is the story of the Time Lords reuniting. This is the new version, revised, improved, and edited. There are some minor, and a few maybe major changes in plot. I don't own Doctor Who, or anything in this really except Chemist, Mechanist, and his TARDIS.
1. Chapter 1

She watched the Dalek scream "Exterminate!" one last time. As she felt her chest, covered, she wanted to scream, she fell back. A man approached her.

"I can help you."

She shut her eyes, and when she opened them, she discovered her wound was healing.

The man was above her, "I am the Soldier. I saved your life, and now you must do something for me."

"What?" she said.

"Help me," he said, "bring victory to the Daleks."

"Yes," she said, willingly.

The Soldier turned to the Chemist, angry.

"We got out," she said.

He placed his hands on her, her skin was now charred. Her body begin to bleed, and the skin cracked. She was so frightened. Her eyes felt dry. She sank to the ground. She saw him walk away.

She croaked, her voice dry, "You said you wouldn't leave me."

"That was a lie," he said.

In the ashes, her body dying. She was not regenerating. She wanted to. Why wasn't she?

The Soldier laughed.

"You have never regenerated, and now you can't!"

Her skin was like bark, and her body was bleeding. When she opened her eyes, the charred skin cracked. Ash had gathered on her body.


	2. Chapter 2

**CHAPTER 2**

Her hair was caked with ash, and her eyes where gently opening as the skin and caked ash cracked. Her eyes looked so tired and only seemed to communicate her pain, dry from it was not black and charred, you could see what was left was blood.

The being who had hurt her was gone. He picked her up and carried her way, this person of honor and glory. He carried her bridal style, wrapping her gently in a silken cloak into his TARDIS. She was dead, but a gentle touch of his hands and regeneration healed her most, deep wounds. Her body turned to a gold, florid net of lines that lit the room. The charred skin begin to change Her body continued to be further engulfed in the energy. She was surrounded by dots of light that orbited, spinning until they hit the ground. She was upheld by the gentle whirl of air. She was being engulfed with the regeneration energy of he who had found her. As the regeneration energy died down, she was a wavy-haired brunette, with fawn-peach skin. Her finder gently moved her hair from her face.

Whispering gently, he said "who are you?" She responded, "a Chemist," (should have said the, but her experiences would have affected her).

He smiled, saying, "I am the Mechanist."

Whining about the pain again as the rest of her body begin to regenerate. The Mechanist held her close to him. She pulled away. She finally stopped.

"The Mechanist!" she said, "I know you, don't I?"

"Yes," he said.

He hugged her, although she was so afraid, and said "I am sorry. I am sorry."

"Do you remember the Doctor?" he said.

"Yes," she said, "he died, didn't he?" suddenly breaking down.

The Mechanist said, "No, I think if we get a hold of him. Would you like to speak to him?"

He handed her the phone, taking it.

"Hello!" she said.

"Hello," said a female voice.

"Doctor?" she said.

"No, I'm Clara," she said, "Here's the Doctor."

"Hello! What do you need?"

"Hello."

"Who is this?"

"The Chemist," she said.

"Really? You are alive?"

"Yes," she said, "I am with the Mechanist. He was wondering where you are?"

"I am," he said, "give the phone to the Mechanist."

"Don't make fun of me because I failed several times in finding locations."

"Shut up! Give him the phone."

She looked at the Mechanist, "He wants me to give you the phone."

The Mechanist plucked the phone out of her hand.

"Where are you?" he asked.

"Well, somehow, the Chemist escaped the time-lock like we both did. One of the planets the Daleks over run before the time lock. She was pretty much dead. Can we meet up somewhere?"

The Mechanist heard the coordinates, and landed his TARDIS, and when the Doctor knocked, he came in followed by Clara.

"Chemist," he said.

"Doctor!" she said, "A bow tie?"

"He thinks it is cool," said the Mechanist.

"It really isn't!" she said.

"Whatever!" he said, "what happened?"

"It's a long story."

The Doctor hugged her once more.

"I have a long story, too, a thousand years of living and running, I got married. Regenerated way too many times! Saved Earth so many times! Oh you have missed so much! This is absolutely cool! Or as I did say: Fantastic! Brilliant! I've met so many people and traveled with," with a melancholy pause before continuing, "currently Clara. Clara! Get in here!"

"Explanation!" she said.

"She's like me! A Time Lord!"

"Okay, do I know you?" said the Chemist.

The Doctor said, "Oh yes, she fell into my timeline and spread herself everywhere to save me! I'm assuming you ran into one of her copies at some point."

The Chemist once more coughed more golden glitter dust, frightening Clara, as the Chemist glowed.

"What is that?" she said, extremely frightened.

"Regeneration energy."

"Who am i?" she demanded.

"You are the Chemist, you have just regenerated."

"Who am I then?"

She crumpled to the floor weeping again.

"I don't even know who I am! Why?" she asked the Mechanist.

She coughed once more, and hoarsely said "Doctor. Mechanist. Clara."

"So where are we going to go now?" asked the Doctor

"Yes, Doctor, where?"

"I have a plan, Chemist and Mechanist, and shush now, Clara. For now, somewhere calm and relaxing for you guys."

"So... where then?" asked the Chemist.

"Its exciting! And you both probably have not gone there! Then again on Gallifrey you can't do anything! It's all boring."


	3. Chapter 3

"Welcome to Atono, a planet of flowers. It has over 5,000 species of flowers!"

"Doctor!" exclaimed both the Chemist and Clara simultaneously.

"Chemist, you should go change out of your still burnt clothing."

"Okay."

They seemed to love each other dearly. He thought of River. He thought of Rose. His own lost loves. He would never truly see River or Rose again. River was dead. Rose was gone. I

t was a valley with grey mountains and a lush green valley; the valley filled with every flowers and roses. Roses where like velvet and silk; flowers were like pastel silk and bright velvet, also.

She looked so happy. She sat down and the Mechanist with her.

Clara and the Doctor were walking about and were laughing at the Mechanist and the Chemist.

"So you aren't one of the two last of the Time Lords anymore."

"I will never be, as there shall never be the last of the Daleks."

"Okay. How do you know her?"

"She went to the Academy with me. Quite odd young girl. I was several grades ahead of her. She wasn't exactly the most socially acceptable."

"Doctor," she said, "You aren't exactly socially acceptable, either."

"Am so. Well I used to be."

"What about them, the Mechanist and Chemist?"

"They fell in love at the Academy when they both reached when he was halfway through intermediate schooling and her going to begin her intermediate schooling. The next year, she was done with intermediate schooling, then she skipped several levels and was above him. But she failed her ability to land the TARDIS where she wanted to, and wouldn't even enter the correct location code."

"You make a habit of taking us to the wrong place, too!" she said.

"It's my TARDIS's fault."

"Whatever."

The Chemist and Mechanist gently laid in the flowers, on his cloak, talking about what happened. How much they had missed one another, their different regenerations. They both had successful life on Gallifrey and had managed to escape.

The Doctor nudged Clara and she woke up, and sat up. The Doctor said, "Come on, sleepy head."

"Doctor... where are we going to now?"

"I have a plan," he said, raising his non-existent eyebrows, "Chemist! Mechanist!"

"What?"

"We are going somewhere different! This is boring! I was hoping something exciting would happen."

"Fine!" said the Mechanist in return, irritated.

"I agree with you!" yelled the Chemist.

Suddenly the Doctor felt like something was looking into his mind. Was this the feeling Clara had described as the feeling like you were being watched.

"Ugh!" said the Chemist, walking back to the TARDIS, mocking the Mechanist.

"Where is my TARDIS?" said the Mechanist.

"You left it remember," she said.

"Oh."

"Sometimes I really question you, Mechanist."

"I have bad memory!"


	4. Chapter 4

**CHAPTER 4**

Italics mean flashbacks

The Doctor said, "we are going to a party."

"Why?"

"Because parties are cool."

The Chemist said, "and you are going like that?"

"Yes," he said, straightening his bow tie.

"Let's go."

Clara tried not to laugh, the Chemist obviously hated his bow tie.

The Doctor stepped out into the party, and as he looked around he yelled, "Jack!"

A still-young looking man looked at him, coming over.

"Who are you?" and upon seeing the TARDIS, he said, well screamed, "DOCTOR!?"

"Yes," he said.

He looked at the Chemist, Mechanist, and Clara.

"Hello, I am Cpt. Jack and you are?"

"Cl-" Clara started.

"No!" said the Doctor.

Cpt, Jack sighed.

"You are still the same!" said the Doctor.

"So are you!" he said, "except much less cute. Why are you wearing a bow tie?"

"It's cool. This is the Chemist, Mechanist, and Clara."

The rest of the evening was spent on the dance floor, and hanging out with people from everywhere.

They met several people. People where either drinking too much, or not drinking at all.

Jack talked to the Doctor about his lack of aging. Clara laughed a bit over the conversation. The Chemist and Mechanist decided to wander off, separately. There was a live performance of different genres of music from each music.

"Give a little, get a lot."

_He looked at her, willing and seemingly kind, she had to trust him. She didn't deserve better. She had lost it all. She would give him everything. He was right. The other non-Daleks were _

"How you live and love"

_She felt like he loved her, but not as she did._

"You aren't funny, you aren't smart, if you think you are going to break my heart"

_She was beginning to feel guilty. She turned around. She could not run._

"I'm not forgetting, I'm not giving up, I'm not weak."

_She threw him to the ground, finally finding courage._

"To think all my life I've been controlled."

_She looked away as he stood up, angry, she felt the feeling of freedom again._

The Chemist woke from her moment. It was the feeling like when you jump up from a dream you are falling in. She felt as if her mind was being looked at. She felt as it seemed every thought was analyzed. Perhaps a telepath was nearby. It seemed to suddenly faded. She walked away.

She looked for the Doctor, and finally found him.


	5. Chapter 5

**CHAPTER 5**

Walking to the console room, the Chemist smiled when she found it. Apparently nobody else was up. She frowned. She looked at the doors. It was a steel wall. This wasn't the console room, but an echo. She exited, and begin to walk down the hallway. Voices filled the corridor, the room spinning. What was happening? She felt as though she was dying. Her body was falling apart into millions of pieces, falling to the floor. Suddenly she was shaken awake, taking a sharp breath in. It was the Mechanist.

"Are you alright?"

"Fine."

They walked to the console room.

"I finally found her," he said.

"Good!" the Doctor said, "we are going someplace I know something will happen! There is a planet of mazes, and nobody knows where they came from and we are going to find out!"

Waking up, her eyes soggy she looked at the Silent. They were in a maze. Running from the Silence.

"You have been here for several weeks," it said gruesomely, before she was grabbed by an arm.

"Clara, come on, I found my TARDIS!"

"Doctor, what about the Mechanist! The Chemist!"

"I found them! Now! Let's go!"

She fainted as soon as she got into the TARDIS she felt so weak. She was shaken awake by the Chemist.

"What happened?"

"Something was chasing us. Some species that we can never remember."

"Doctor, are you okay?"

"No, obviously I'm fine!"

"Doctor, please relax," she said, at his side at that moment, "It is no use being angry."

"River is still in there. I saw her!"

"Okay. Let's go find her."

"We can't, we can't loose the TARDIS."

"Scan for her."

"I am right now Clara!" he yelled at her.

"Okay," she said, still hurt.

She wanted to cry, the Doctor never yelled at her. He turned around as she walked out the door.

"I can't find her!"

The Chemist said, "Are you sure she is there?"

"Yes!" he said.

Hours passed, and he still could not find her.


	6. Chapter 6

**CHAPTER 6**

Clara and the Chemist get to have girl talk alone

"Clara," she said, "what do you think of the Doctor."

"He acts like a 10 year old."

"You don't like him?" she asked.

"I don't like him," she said.

"Why not?"

"I don't know. Not my type. He is cute. Quite cute."

"You do like him."

"Nope," she said.

"Denial!" she teased back.

"Clara?" said the Chemist, shaking her.

"What?" she said.

"You seem preoccupied. Told you that you were in denial."

"Sorry. What about you and the Mechanist?"

"I don't know, sometimes I feel like I don't love him."

"Oh..." she said.

"But then he will say something and I fall right back in love with him. I feel like he is drifting away. I feel so unwanted and unnecessary. He occasionally just ignores me. It hurts. And then I m back out of love. He always has a good reason, however, I feel like I make excuses for myself. He thinks he is so safe, but I will break up with him and stay with the Doctor and let him venture off in his own TARDIS if it doesn't change."

Clara looked rather surprised, but a knock at the door ended the conversation.

"Mechanist," she said.

"The Doctor wants to take us to London."

"Is he going to try again," said Clara.

"And he wants you two to change into more time-appropriate clothing. 1895, apparently."

He closed the door.

The Chemist and Clara went off in search of the TARDIS's massive wardrobe.

"Corsets," said the Chemist with a dramatic sigh.

"Again?" said Clara.

"Apparently."

The Chemist went off in search of a corset.

A half hour passed.

"How did Victorian women wear these?" she said, frowning.

"I don't know. I have worn them now twice, too."

The Doctor walked in what he always wore, and said, "Come on!"

"Why don't you change?"

"Because I already am fine."

"Ugh!" said the Chemist.

"Who are you?"

"The Chemist."

"Doctor, Clara, Mechanist."

"Yes, can we stay with you?" asked the Mechanist.

"Of course. Strax, can you help them?"

"I'll get some grenades, arsenic vapor, cyanide powder, and pistols for them ma'am!"

"Strax! Help them find a room. Jenny. Help Strax."

"Yes ma'am. This way. Clara, Chemist you can share this room. Mechanist, Doctor, you can have this room." Both rooms had 2 large beds a night stand.

The Doctor sat, something was going on. It felt fake and weird to be here. He felt as though these thoughts were unnatural and wrong, but yet somehow undeniable. Life had been so fake and artificial since Atono.

The Mechanist noticed the Doctor was sitting still and thinking.

"Doctor!"

"Yes?" he said interrupted.

"You okay?

"No. Doesn't everything seem different since Atono?"

"I don't know, what do you mean. The addition of the Chemist?"

"No. Different."

"No, why?"

The Chemist walked in.

"Hello, Doctor and Mechanist."

The Chemist sat by the Mechanist, who seemed tired, however, placed his arm casually around her.

Clara said, "Can you take me home and give me a break for a day or two?"

"Yes," he said, opening the doors of the TARDIS.

She stepped out, and said, "see you."

He closed the doors.


	7. Chapter 7

**CHAPTER 7**

Clara woke up. It had been several days since she had seen the Doctor. Perhaps the TARDIS was making it difficult.

"Doctor," said the Chemist, "when are you going to pick up Clara?"

"We aren't."

"Doctor?"

"I left her behind," he said, "I will take you and the Mechanist back to his TARDIS."

"Doctor!" she said, surprised.

He piloted the TARDIS landing it by the Mechanist's telling them to go. He then landed the TARDIS back in a familiar cloud, except slightly different in location. He sat in his TARDIS room, head in his hands, straightening his bow tie. He felt so broken. He lost everyone, either leaving them behind or could not see them again. The TARDIS whined. He looked up at the console.

"Mechanist!" she said, "take me to Clara."

"Why?"

"The Doctor is leaving her behind."

"Why?"

"I don't know. Is all you can say why?"

"Why?"

"Shut up," she said.

"Why?" he said, and was surprised by a kiss.

"Now take me."

"I will."

They landed, a week and a half after the Doctor had left. They knocked on the door.

"Hello," said a young boy.

"Where is Clara?"

"Upstairs. Why?"

"Can we talk to her?"

"Clara!" he said, yelling up the stairs.

Clara came down, and when she saw them she ran down.

She came out with them.

"Where is the Doctor?"

"If we knew, we would tell you," they said.

"What do you mean?"

"He isn't coming back," the Chemist said.

Clara looked unsure.

"He decided to leave you."

Clara put her head in her hands.

"How can we find him?"

"Come with us."

Clara joined them in them in his fridge TARDIS.

Clara made a strange look.

"I know! You couldn't see it earlier."

He opened one door. "Oops," he said shutting it. He then opened the other one and stepped into it. Clara and the Chemist followed.

The console was a large metal octagon. The center was a clear cylinder, the interior of it had a oddly shaped, looking like silver stacked circle. Steam like gas emerged from the top of the center. The walls were very oddly shaped metallic. Around the console, there were multiple panels. 3 other doorways suggested other rooms.

"How do we find him?"

"Well," the Chemist said, "I don't know. Suggestions?"

"No," she said.

The Mechanist said, "I think if we look at the Time Vortex we can look for the TARDIS's trail."  
"So, what type of TARDIS is this? It hasn't growled at me yet, though."

"Earlier than the Doctor's. A Type-23. There were 8 actually used before and including the Type-40: type-1, type-14, type-21, type-23, type-32, and type-39. Most of them don't exist. There are quite a few type-23s. They are extremely inexpensive."

"He's cheap," the Chemist said.

"Actually, I stole it," he corrected, "from my parents."

"Still cheap," she said.

Clara smiled.

"I think I found it."

The screen displayed what appeared to be a wavy snowstorm of different colors.

Clara gave a questioning look.

"Certain patterns in the time winds and vortex," he said pointing at a set of swirling lines," he said.

Upon touching the screen, 2 line formed around the odd phenomenal, the analysis appeared, in Gallifreyan. He pressed one of them, and the TARDIS begin to whirr. Unlike the Doctor's, it was obnoxious, and not at all nice to listen to. It was like when breaks squeaked in a car.

They landed.

"We are back in Victorian London."

"I have still have my dress on."

"Why didn't you take it off?"

"We went for you as soon as we could," she said, "however, these corsets are quite irritating."

They stepped out.

They went to look for Madame Vastra, Strax, and Jenny. They always knew where the Doctor was. Even they did not know where he was.

"Ugh!" said the Mechanist.

The Doctor heard the phone ring. He heard the TARDIS whine when he did not answer it. He listened to the voice on the other end, as a voice message was left.

"Doctor," said the Mechanist, "Where are you?"

He looked down. He could lose Clara, the Chemist, and the Mechanist. He had lost River, Amy, and Rory. He always lost people. He had always lived on. Why? Why couldn't he die and leave them behind? He could die. The Master did, even though he could regenerate. He had stopped it. He went to the console. He couldn't stay here. He went to the console. He piloted the TARDIS. The TARDIS alerted him to the presence of the Mechanist's TARDIS. He landed the TARDIS immediately, but discovered that the Mechanist had also seen him. He went to the doors, verifying they were locked. He sighed, walking away into the corridors of the TARDIS, seeking a way out.

The Mechanist said, "there he is!"

He ran around the TARDIS, going back to the screen. They stepped out, not caring where or when they were, banging on the blue TARDIS doors. The Doctor heard it, and the TARDIS whined again. The Doctor walked down the hallways.

The Chemist banged on the Door.

"Doctor," she said.

The TARDIS made a strange whine. The Chemist tried to find the TARDIS key in her pocket, but quickly discovered that one: the dress did not have pockets and two: he had taken the key. She shook the TARDIS doors, they continued to refuse entrance.

Suddenly the doors were opened by a blonde woman.


	8. Chapter 8

**CHAPTER 8**

"I don't know how, but I was in the library but now I'm here. Where is the Doctor?"

"We are trying to find him!" she desperately said.

"Why?"

"He left behind Clara and us. Somethings wrong."

River looked concerned, letting them in. They went down one of the many hallways, looking for him. River was wearing an odd spacesuit like outfit. River pulled out her own sonic screwdriver, as well as the Mechanist. They found he was on the other side of a door, which they opened as quickly as they could.

"The swimming pool?"

The TARDIS whined loudly.

"Doctor!" said Clara running to the pool, diving in.

"Clara!" said River, the Chemist, and Mechanist, running after her.

Clara saw the Doctor under the water, halfway floating, halfway sinking. She swam down to him, grabbing him, and trying to pull him to the surface. The water was freezing. She pulled him up to the surface and letting go, it was exhausting. She felt yanked out of the water by the Mechanist, who also tried to yank out the Doctor.

River helped him, placing her head on his chest. She looked at him, waiting desperately. He coughed looking up, whimpering, "River? Am I dead?"

She sighed. Clara was laying on her back, off to side, drenched. She shivered, happy to see the Doctor alive. River slapped him.

"Doctor," she said.

"How are you here?"

"I was in the library, then I was here."

"How did you get in?" he demanded.

"Me," said River.

"Why did you follow me?"

"You left Clara behind and us," said the Chemist, "what's going on?"

The Doctor said,"where is Clara?"

"We have her."

He coughed, getting up his heavy coat dripping. He became quickly aware of what River was wearing.

"River," he said, "You shouldn't even be here."

She said, "Well, I suppose I should be off then. I suppose you don't want to know."

"What?"

She had a vortex manipulator, taking it in her hands she disappeared.

The Doctor seemed to sigh with relief, and went over to Clara.

She looked angry.

"Doctor," she said, "I just saved your life. Again."

He picked her up, hugging her, "I'm losing everyone. I couldn't lose you or the Chemist or the Mechanist."

"Doctor," she said, not knowing what else to say. The Chemist hugged the Mechanist, and was relieved. The Doctor looked at her, saddened by how much he had hurt her. Clara shivered.

"I'm sorry," she finally said, however, she desired to slap him internally.

The Doctor said, "thank you," placing his head against her head.


End file.
